Document Inquiry Poses Unparalleled Test for Justice Dept.

WASHINGTON — As Justice Department officials haggled for months this year with former President Donald J. Trump’s lawyers and aides over the return of government documents at his Florida home, federal prosecutors became convinced that they were not being told the whole truth.

That conclusion helped set in motion a decision that would amount to an unparalleled test of the Justice Department’s credibility in a deeply polarized political environment: to seek a search warrant to enter Mar-a-Lago and retrieve what prosecutors suspected would be highly classified materials, beyond the hundreds of pages that Mr. Trump had already returned.

By the government’s account, that gamble paid off, with F.B.I. agents carting off boxloads of sensitive material during the search three weeks ago, including some documents with top secret markings.

But the matter hardly ended there: What had started as an effort to retrieve national security documents has now been transformed into one of the most challenging, complicated and potentially explosive criminal investigations in recent memory, with tremendous implications for the Justice Department, Mr. Trump and public faith in government.

Attorney General Merrick B. Garland now faces the prospect of having to decide whether to file criminal charges against a former president and likely 2024 Republican candidate, a step without any historical parallel.

Remarkably, he may have to make this choice twice, depending on what evidence his investigators find in their separate, broad inquiry into Mr. Trump’s efforts to reverse the outcome of the 2020 election and his involvement with the Jan. 6 attack on the Capitol.

The department’s Jan. 6 investigation began as a manhunt for the rioters who attacked the Capitol. But last fall it expanded to include actions that occurred before the assault, such as the plan to submit slates of electors to Congress that falsely stated Mr. Trump had won in several key swing states.

This summer, prosecutors in the U.S. attorney’s office in Washington began to ask witnesses directly about any involvement by Mr. Trump and members of his inner circle, including the former White House chief of staff Mark Meadows, had in efforts to reverse his election loss.

For all his efforts to distance the department from politics, Mr. Garland cannot escape the political repercussions of his decisions. How he handles Mr. Trump will surely define his tenure.

It is still unclear how either case will play out. Prosecutors working on the investigation into Mr. Trump’s handling of classified information are nowhere near making a recommendation to Mr. Garland, according to people with knowledge of the inquiry. Court filings describe the work as continuing, with the possibility of more witness interviews and other investigative steps to come.

So far, Mr. Garland has signaled that he is comfortable with owning all of the decisions related to Mr. Trump. He has resisted calls to appoint a special counsel to deal with investigations into the former president. In his first speech to the department’s 115,000 employees last year, he expressed faith that together they could handle any case. “All of us are united by our commitment to the rule of law and to seeking equal justice under law,” he said.

Over the course of this year, as prosecutors sought to understand how sensitive government documents ended up at Mr. Trump’s Florida resort, they began to examine whether three laws had been broken: the Espionage Act, which outlaws the unauthorized retention or disclosure of national security information; a law prohibiting the mishandling of sensitive government records; and a law against obstructing a federal investigation.

By summertime, the investigation into Mr. Trump’s handling of classified information had started to yield compelling indications of possible intent to thwart the law, according to two people familiar with the work. While there was not necessarily ironclad evidence, witness interviews and other materials began to point to the possibility of deliberate attempts to mislead investigators. In addition to witness interviews, the Justice Department obtained security camera footage of various parts of Mar-a-Lago from the Trump Organization.

The heavily redacted affidavit explaining the government’s desire for a search warrant said that the Justice Department had “probable cause to believe that evidence of obstruction will be found at” Mar-a-Lago, and that “the government has well-founded concerns that steps may be taken to frustrate or otherwise interfere with this investigation if facts in the affidavit were prematurely disclosed.”

But a decision about whether to charge Mr. Trump over attempts to obstruct the investigation, or his handling of sensitive national security information, would involve a variety of considerations.

At the heart of the case would be evidence uncovered by the F.B.I., which is still trying to understand how and why government records made their way to Mar-a-Lago and why some remained there despite repeated requests for their return by the National Archives and a later subpoena from the Justice Department.

But the highly classified nature of some of the documents retrieved from Mar-a-Lago and the possible evidence of obstruction are only some elements that will go into any final decision about pursuing a prosecution.

Career national security prosecutors will conduct a robust analysis of whether that evidence persuasively shows that laws were broken. That process will include a look at how the facts have been applied in similar cases brought under those same laws, information that prosecutors examined when they investigated former Secretary of State Hillary Clinton and the former C.I.A. director David H. Petraeus.

In the case involving Mrs. Clinton’s use of a private email server, for instance, officials in the national security division asked prosecutors to dive deep into the history of the Espionage Act. At issue was whether her handling of classified information indicated she had engaged in gross negligence. One compelling case of gross negligence that they did find, involving a former F.B.I. agent, included far more serious factors. After examining past examples, they found that her case did not meet that standard. In the end, the consensus was not to charge Mrs. Clinton.

But Mr. Trump’s case presents the additional question of obstruction of justice, and the possibility that evidence could show that he or his legal team defied the Justice Department to hold onto documents that belonged to the government.

That in some ways echoes a previous obstruction inquiry conducted by Robert S. Mueller III, the special counsel who examined whether Russia interfered in the 2016 election. His final report showed that Mr. Trump tried to curtail, or even end, the special counsel inquiry as he learned more about it. But Mr. Mueller declined to say whether Mr. Trump had broken the law, allowing the attorney general at the time, William P. Barr, to clear Mr. Trump of that crime.

There is no way to know whether the Justice Department has facts regarding obstruction that meet its standard of prosecution, which is evidence that would “probably be sufficient to obtain and sustain a conviction.”

But the Justice Department’s own legal filings have thrust the question of obstruction into public view. Should Mr. Garland find that there is not enough evidence to indict Mr. Trump, the Justice Department under two successive administrations will have chosen not to recommend prosecuting Mr. Trump for that crime.

If Mr. Garland chooses to move forward with charges, it will be a historic moment for the presidency, a former leader of the United States accused of committing a crime and possibly forced to defend himself before a jury of his fellow citizens. It is a process that could potentially unfold even as he runs again for the White House against an incumbent whose administration is prosecuting him.

That, too, runs huge risks for the department’s credibility, particularly if the national security threat presented by Mr. Trump’s possession of the documents, inevitably disclosed at least in part during the course of any trial, do not seem substantial enough to warrant such a grave move.

Mr. Garland and his investigators are fully aware of the implications of their decisions, according to people familiar with their work. The knowledge that they will be scrutinized for impropriety and overreach, they say, has underscored the need to hew to the facts.

But a decision to prosecute — or to decline to prosecute — has political implications that Mr. Garland cannot escape. And no matter of judiciousness can change the fact that he is operating within an America as politically divided as it has been in decades.

Mr. Trump’s supporters have viewed any investigative steps around the former president as illegitimate attacks by a partisan Justice Department that is out to get him. And his detractors believe that any decision not to prosecute, no matter the evidence, would show that Mr. Trump is indeed above the law.